Genome-wide identification of MATH-BTB gene family and expression analysis in rye (Secale cereale L.)

Proteins encoded by the MATH-BTB gene family regulate plant grain development by mediating the degradation of transcription factors. This study identified the MATH-BTB family in rye through a homology-based search and performed a bioinformatic analysis to investigate its functions. We identified 56 MATH-BTB genes in the rye genome. Phylogenetic analysis classified these genes into 10 distinct subfamilies. Synteny analysis revealed​no collinear genes with Arabidopsis or maize, one with rice, and 16 with the A subgenome of wheat. Cluster analysis of expression data revealed that this gene family is predominantly expressed in spikes and grains, suggesting its potential role in grain development. Integration with our previous findings on yield-related traits pinpointed a specific MATH-BTB gene, ScWN4R01G352500.1 , which was previously associated with grain width.. This strengthens the hypothesis that this gene family plays a role in grain development. Furthermore, we developed a Kompetitive Allele-Specific PCR (KASP) marker that effectively genotypes the grain width trait. Collectively, these results provide a valuable resource for future functional studies of the MATH-BTB family in rye and offer a directly applicable marker for molecular breeding programs aimed at improving grain width.